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RiboParser

4.6.1 Gene quantification

Renscq/RiboParser

4.6.1 Gene quantification¶

Function¶

rpf_Quant quantifies RPF density at gene or transcript level. It summarizes CDS reads by default and can also quantify UTR regions when the corresponding options are enabled.

The command reports raw RPF counts, RPM, RPKM, and TPM tables, and draws basic sample-level QC plots based on CDS RPM values.

Input files¶

Input	Required	Description
Merged density table	Yes	RPF density table generated by `rpf_Merge`, usually `RIBO_merged.txt`. The table should contain annotation columns followed by per-sample frame columns.

Parameters¶

Parameter	Required	Description
`-r`	Yes	Input RPF density table in TXT format.
`-o`	Yes	Output prefix.
`-f`	No	Reading frame used for quantification. Choices: `0`, `1`, `2`, `all`. Default: `all`.
`--tis`	No	Number of codons after the translation initiation site to discard before CDS quantification. Default: `0`.
`--tts`	No	Number of codons before the translation termination site to discard before CDS quantification. Default: `0`.
`--utr5`	No	Enable additional 5'UTR-related quantification. Disabled by default.
`--utr3`	No	Enable additional 3'UTR-related quantification. Disabled by default.

Output files¶

Assuming -o RIBO, the command writes:

Output	Description
`RIBO_total.txt`	Total RPF count summary for each sample.
`RIBO_cds_rpf_quant.txt`	Raw CDS RPF count table.
`RIBO_cds_rpm_quant.txt`	CDS RPM table.
`RIBO_cds_rpkm_quant.txt`	CDS RPKM table.
`RIBO_cds_tpm_quant.txt`	CDS TPM table.
`RIBO_cds_rpm_bar_plot.pdf`	Stacked bar plot showing the proportion of reads in transcript regions.
`RIBO_cds_rpm_cdf_plot.pdf`	Empirical cumulative distribution plot of log2-transformed CDS RPM values.
`RIBO_cds_rpm_pca_plot.pdf`	PCA plot based on log2-transformed CDS RPM values.
`RIBO_cds_rpm_pca.txt`	PCA coordinates for samples.
`RIBO_cds_rpm_heatmap.pdf`	Heatmap of scaled CDS RPM values.
`RIBO_utr5_*_quant.txt`	Optional 5'UTR quantification tables when UTR quantification is enabled.
`RIBO_utr3_*_quant.txt`	Optional 3'UTR quantification tables when UTR quantification is enabled.

Example¶

rpf_Quant \
    -r ../05.merge/RIBO_merged.txt \
    --tis 15 \
    --tts 5 \
    -f 0 \
    -o RIBO \
    &> RIBO.quant.log

Notes¶

--tis and --tts are recommended for CDS quantification because start- and stop-proximal codons often show strong biological and technical biases.
-f 0 is commonly used for canonical P-site CDS quantification when the upstream offset and periodicity analysis support frame 0.
Current implementation always runs CDS quantification. UTR output depends on the UTR options and should be checked carefully when UTR-specific results are needed.

Use merge_quant to merge multiple quantification tables:

Parameters¶

Parameter	Required	Description
`-l`, `--list`	Yes	One or more quantification result files, for example `*_rpf_quant.txt`.
`-o`	Yes	Output prefix. The merged table is written as `<prefix>_rpf_quant.txt`.

Example¶

merge_quant \
    -l *_cds_rpf_quant.txt \
    -o merged_cds